The RNA sequence of HIV-1 TAR was systematically altered to change its propensity to adopt a functional secondary structure in the ensemble, measured using 1H CEST NMR. These minor sequence changes shifted the active-state propensity by ∼500-fold, quantitatively predicting changes in protein binding and cellular transactivation. These propensities could be inferred from secondary-structure prediction algorithms and incorporated into a thermodynamic framework to quantitatively predict how sequence changes alter protein-binding affinity and RNA cellular activity.
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Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles – Research
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